mmLib.TLS.TLSFileFormatPDB

Package mmLib :: Module TLS :: Class TLSFileFormatPDB

[show private | hide private]

Type TLSFileFormatPDB

     object --+    
              |    
RecordProcessor --+
                  |
     object --+   |
              |   |
  TLSFileFormat --+
                  |
                 TLSFileFormatPDB

Reads TLS descriptions from the REMARK records in PDB files. These records are only written by REFMAC5.

Method Summary
	`complete_L(self)`
	`complete_S(self)`
	`complete_T(self)`
	`load(self, fil)` Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.
	`load_supported(self)` Returns True if file loading is supported, otherwise returns False.
	`process_REMARK(self, rec)` Callback for the PDBFile parser for REMARK records.
Inherited from TLSFileFormat
	`save(self, fil, tls_desc_list)` Writes the list of TLSGroupDesc object to the given file.
	`save_supported(self)` Return True if file saving is supported, otherwise returns False.
Inherited from RecordProcessor
	`preprocess_default(self, rec)`
	`process_ATOM(self, rec)`
	`process_default(self, rec)`
	`process_pdb_records(self, pdb_rec_iter, filter_func)` Iterates the PDB records in self, and searches for handling methods in the processor object for reading the objects.
Inherited from object
	`__init__(...)` x.__init__(...) initializes x; see x.__class__.__doc__ for signature
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
	`__str__(x)` x.__str__() <==> str(x)

Class Variable Summary
`dict`	`pdb_regex_dict` = `{'origin': <_sre.SRE_Pattern object at ...`

Method Details

load(self, fil)

Returns a list containing one TLSGroupDesc object for each TLS group description found in the file.

Overrides:: mmLib.TLS.TLSFileFormat.load (inherited documentation)

load_supported(self)

Returns True if file loading is supported, otherwise returns False.

Overrides:: mmLib.TLS.TLSFileFormat.load_supported (inherited documentation)

process_REMARK(self, rec)

Callback for the PDBFile parser for REMARK records. If the REMARK records contain TLS group information, then it is extracted and added to the TLSGroups list.

Class Variable Details

pdb_regex_dict

Type:: dict
Value:: {'group': <_sre.SRE_Pattern object at 0xb7941620>, 'l11_l22': <_sre.SRE_Pattern object at 0xb7979210>, 'l13_l23': <_sre.SRE_Pattern object at 0xb7979400>, 'l33_l12': <_sre.SRE_Pattern object at 0xb7979308>, 'origin': <_sre.SRE_Pattern object at 0x91d5768>, 'range': <_sre.SRE_Pattern object at 0x9148360>, 's11_s12_s13': <_sre.SRE_Pattern object at 0x905faf8>, 's21_s22_s23': <_sre.SRE_Pattern object at 0x910a268>, ...

Generated by Epydoc 2.1 on Sun Apr 23 22:08:39 2006

http://epydoc.sf.net